Hi Doug,
I was running preproc-sess in the newly released freesurfer-5.2.0. The command I used was:
preproc-sess -sf sessid -df sessdir -fsd bold -surface fsaverage lhr -mni305 -fwhm 6 -per-run
The program failed with the following errors:
3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save 004/fmcpr.mat -base 004/tmp.mc-afni2.29239/tempvol.nii.gz -prefix 004/tmp.mc-afni2.29239/outvol.nii.gz 004/tmp.mc-afni2.29239/invol.nii.gz 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr ERROR: 3dvolreg.afni Invalid null command.
I have the file 3dvolreg.afni in $FREESURFER_HOME/bin. There is another file of the same name under afni/bin. Preproc-sess is relying on the version in $FREESURFER_HOME/bin.
Do you know what the problem is? Should I replace freesurfer's copy of 3dvolreg.afni with AFNI's copy of 3dvolreg.afni?
Thanks.
-Yuhong
Hi Yuhong, What happens when you run 3dvolreg.afni from the command line without any args? doug
On 03/21/2013 12:38 PM, Y.V. Jiang wrote:
Hi Doug,
I was running preproc-sess in the newly released freesurfer-5.2.0. The command I used was:
preproc-sess -sf sessid -df sessdir -fsd bold -surface fsaverage lhr -mni305 -fwhm 6 -per-run
The program failed with the following errors:
3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save 004/fmcpr.mat -base 004/tmp.mc-afni2.29239/tempvol.nii.gz -prefix 004/tmp.mc-afni2.29239/outvol.nii.gz 004/tmp.mc-afni2.29239/invol.nii.gz 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr ERROR: 3dvolreg.afni Invalid null command.
I have the file 3dvolreg.afni in $FREESURFER_HOME/bin. There is another file of the same name under afni/bin. Preproc-sess is relying on the version in $FREESURFER_HOME/bin.
Do you know what the problem is? Should I replace freesurfer's copy of 3dvolreg.afni with AFNI's copy of 3dvolreg.afni?
Thanks.
-Yuhong
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thanks for the reply. From the command line the command 3dvolreg.afni returned the following error:
3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr
-Yuhong
On Thu, Mar 21, 2013 at 12:08 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Hi Yuhong, What happens when you run 3dvolreg.afni from the command line without any args? doug
On 03/21/2013 12:38 PM, Y.V. Jiang wrote:
Hi Doug,
I was running preproc-sess in the newly released freesurfer-5.2.0. The command I used was:
preproc-sess -sf sessid -df sessdir -fsd bold -surface fsaverage lhr -mni305 -fwhm 6 -per-run
The program failed with the following errors:
3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save 004/fmcpr.mat -base 004/tmp.mc-afni2.29239/tempvol.nii.gz -prefix 004/tmp.mc-afni2.29239/outvol.nii.gz 004/tmp.mc-afni2.29239/invol.nii.gz 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr ERROR: 3dvolreg.afni Invalid null command.
I have the file 3dvolreg.afni in $FREESURFER_HOME/bin. There is another file of the same name under afni/bin. Preproc-sess is relying on the version in $FREESURFER_HOME/bin.
Do you know what the problem is? Should I replace freesurfer's copy of 3dvolreg.afni with AFNI's copy of 3dvolreg.afni?
Thanks.
-Yuhong
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
what platform are you using?
On 03/21/2013 01:24 PM, Y.V. Jiang wrote:
Hi Doug,
Thanks for the reply. From the command line the command 3dvolreg.afni returned the following error:
3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr
-Yuhong
On Thu, Mar 21, 2013 at 12:08 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Yuhong, What happens when you run 3dvolreg.afni from the command line without any args? doug On 03/21/2013 12:38 PM, Y.V. Jiang wrote: > Hi Doug, > > I was running preproc-sess in the newly released freesurfer-5.2.0. The > command I used was: > > preproc-sess -sf sessid -df sessdir -fsd bold -surface fsaverage lhr > -mni305 -fwhm 6 -per-run > > The program failed with the following errors: > > 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save > 004/fmcpr.mat -base 004/tmp.mc-afni2.29239/tempvol.nii.gz -prefix > 004/tmp.mc-afni2.29239/outvol.nii.gz 004/tmp.mc-afni2.29239/invol.nii.gz > 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: > afni_ncerr > ERROR: 3dvolreg.afni > Invalid null command. > > I have the file 3dvolreg.afni in $FREESURFER_HOME/bin. There is > another file of the same name under afni/bin. Preproc-sess is relying > on the version in $FREESURFER_HOME/bin. > > Do you know what the problem is? Should I replace freesurfer's copy of > 3dvolreg.afni with AFNI's copy of 3dvolreg.afni? > > Thanks. > > -Yuhong > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Doug,
I am using Linux: x86_64 GNU/Linux. Thanks.
-Yuhong
On Thu, Mar 21, 2013 at 12:57 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
what platform are you using?
On 03/21/2013 01:24 PM, Y.V. Jiang wrote:
Hi Doug,
Thanks for the reply. From the command line the command 3dvolreg.afni returned the following error:
3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr
-Yuhong
On Thu, Mar 21, 2013 at 12:08 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
Hi Yuhong, What happens when you run 3dvolreg.afni from the command line without any args? doug On 03/21/2013 12:38 PM, Y.V. Jiang wrote: > Hi Doug, > > I was running preproc-sess in the newly released freesurfer-5.2.0. The > command I used was: > > preproc-sess -sf sessid -df sessdir -fsd bold -surface fsaverage lhr > -mni305 -fwhm 6 -per-run > > The program failed with the following errors: > > 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save > 004/fmcpr.mat -base 004/tmp.mc-afni2.29239/**tempvol.nii.gz -prefix > 004/tmp.mc-afni2.29239/outvol.**nii.gz 004/tmp.mc-afni2.29239/invol.**nii.gz > 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: > afni_ncerr > ERROR: 3dvolreg.afni > Invalid null command. > > I have the file 3dvolreg.afni in $FREESURFER_HOME/bin. There is > another file of the same name under afni/bin. Preproc-sess is relying > on the version in $FREESURFER_HOME/bin. > > Do you know what the problem is? Should I replace freesurfer's copy of > 3dvolreg.afni with AFNI's copy of 3dvolreg.afni? > > Thanks. > > -Yuhong > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
which version of CentOS? Also, can you send me the result of cat $FREESURFER_HOME/build-stamp.txt
On 03/21/2013 02:09 PM, Y.V. Jiang wrote:
Hi Doug,
I am using Linux: x86_64 GNU/Linux. Thanks.
-Yuhong
On Thu, Mar 21, 2013 at 12:57 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
what platform are you using? On 03/21/2013 01:24 PM, Y.V. Jiang wrote: Hi Doug, Thanks for the reply. From the command line the command 3dvolreg.afni returned the following error: 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr -Yuhong On Thu, Mar 21, 2013 at 12:08 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: Hi Yuhong, What happens when you run 3dvolreg.afni from the command line without any args? doug On 03/21/2013 12:38 PM, Y.V. Jiang wrote: > Hi Doug, > > I was running preproc-sess in the newly released freesurfer-5.2.0. The > command I used was: > > preproc-sess -sf sessid -df sessdir -fsd bold -surface fsaverage lhr > -mni305 -fwhm 6 -per-run > > The program failed with the following errors: > > 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save > 004/fmcpr.mat -base 004/tmp.mc-afni2.29239/tempvol.nii.gz -prefix > 004/tmp.mc-afni2.29239/outvol.nii.gz 004/tmp.mc-afni2.29239/invol.nii.gz > 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: > afni_ncerr > ERROR: 3dvolreg.afni > Invalid null command. > > I have the file 3dvolreg.afni in $FREESURFER_HOME/bin. There is > another file of the same name under afni/bin. Preproc-sess is relying > on the version in $FREESURFER_HOME/bin. > > Do you know what the problem is? Should I replace freesurfer's copy of > 3dvolreg.afni with AFNI's copy of 3dvolreg.afni? > > Thanks. > > -Yuhong > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Hi Doug,
Here's the output from cat /proc/version:
Linux version 2.6.32-45-generic (buildd@batsu) (gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5.1) ) #101-Ubuntu SMP Mon Dec 3 15:39:38 UTC 2012
This is the result of cat $FREESURFER_HOME/build-stamp.txt
freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0
Thanks.
-Yuhong
On Thu, Mar 21, 2013 at 1:12 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
which version of CentOS? Also, can you send me the result of cat $FREESURFER_HOME/build-stamp.**txt
On 03/21/2013 02:09 PM, Y.V. Jiang wrote:
Hi Doug,
I am using Linux: x86_64 GNU/Linux. Thanks.
-Yuhong
On Thu, Mar 21, 2013 at 12:57 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
what platform are you using? On 03/21/2013 01:24 PM, Y.V. Jiang wrote: Hi Doug, Thanks for the reply. From the command line the command 3dvolreg.afni returned the following error: 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr -Yuhong On Thu, Mar 21, 2013 at 12:08 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>wrote:
Hi Yuhong, What happens when you run 3dvolreg.afni from the command line without any args? doug On 03/21/2013 12:38 PM, Y.V. Jiang wrote: > Hi Doug, > > I was running preproc-sess in the newly released freesurfer-5.2.0. The > command I used was: > > preproc-sess -sf sessid -df sessdir -fsd bold -surface fsaverage lhr > -mni305 -fwhm 6 -per-run > > The program failed with the following errors: > > 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save > 004/fmcpr.mat -base 004/tmp.mc-afni2.29239/**tempvol.nii.gz -prefix > 004/tmp.mc-afni2.29239/outvol.**nii.gz 004/tmp.mc-afni2.29239/invol.**nii.gz > 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: > afni_ncerr > ERROR: 3dvolreg.afni > Invalid null command. > > I have the file 3dvolreg.afni in $FREESURFER_HOME/bin. There is > another file of the same name under afni/bin. Preproc-sess is relying > on the version in $FREESURFER_HOME/bin. > > Do you know what the problem is? Should I replace freesurfer's copy of > 3dvolreg.afni with AFNI's copy of 3dvolreg.afni? > > Thanks. > > -Yuhong > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting><http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html><http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Hmmmm, it looks like you are missing a library. Do you have afni installed? Maybe Nick or Zeke can chime in. He's getting the following error:
3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr
When I run it on minerva (which I think is centos4.0 x64) I get: /space/freesurfer/centos4.0_x86_64/stable5_2_0/bin/3dvolreg.afni /space/freesurfer/centos4.0_x86_64/stable5_2_0/bin/3dvolreg.afni: error while loading shared libraries: requires glibc 2.5 or later dynamic linker
There is the same error when I run 3dvolreg from minerva: /usr/pubsw/packages/AFNI/2011_12_21_1014/3dvolreg
Maybe our version of AFNI cannot be run under centos4?
Yuhong, if you download and install AFNI (or if you have it), you can copy 3dvolreg to $FREESURFER_HOME/bin/3dvolreg.afni
doug
On 03/21/2013 02:14 PM, Y.V. Jiang wrote:
Hi Doug,
Here's the output from cat /proc/version:
Linux version 2.6.32-45-generic (buildd@batsu) (gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5.1) ) #101-Ubuntu SMP Mon Dec 3 15:39:38 UTC 2012
This is the result of cat $FREESURFER_HOME/build-stamp.txt
freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0
Thanks.
-Yuhong
On Thu, Mar 21, 2013 at 1:12 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
which version of CentOS? Also, can you send me the result of cat $FREESURFER_HOME/build-stamp.txt On 03/21/2013 02:09 PM, Y.V. Jiang wrote: Hi Doug, I am using Linux: x86_64 GNU/Linux. Thanks. -Yuhong On Thu, Mar 21, 2013 at 12:57 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: what platform are you using? On 03/21/2013 01:24 PM, Y.V. Jiang wrote: Hi Doug, Thanks for the reply. From the command line the command 3dvolreg.afni returned the following error: 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr -Yuhong On Thu, Mar 21, 2013 at 12:08 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: Hi Yuhong, What happens when you run 3dvolreg.afni from the command line without any args? doug On 03/21/2013 12:38 PM, Y.V. Jiang wrote: > Hi Doug, > > I was running preproc-sess in the newly released freesurfer-5.2.0. The > command I used was: > > preproc-sess -sf sessid -df sessdir -fsd bold -surface fsaverage lhr > -mni305 -fwhm 6 -per-run > > The program failed with the following errors: > > 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save > 004/fmcpr.mat -base 004/tmp.mc-afni2.29239/tempvol.nii.gz -prefix > 004/tmp.mc-afni2.29239/outvol.nii.gz 004/tmp.mc-afni2.29239/invol.nii.gz > 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: > afni_ncerr > ERROR: 3dvolreg.afni > Invalid null command. > > I have the file 3dvolreg.afni in $FREESURFER_HOME/bin. There is > another file of the same name under afni/bin. Preproc-sess is relying > on the version in $FREESURFER_HOME/bin. > > Do you know what the problem is? Should I replace freesurfer's copy of > 3dvolreg.afni with AFNI's copy of 3dvolreg.afni? > > Thanks. > > -Yuhong > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Y.V. Jiang